Description Usage Arguments Value Examples
View source: R/estimateParams.R
It is used to estimate pulse model parameters. Transcription rates, processing rates, and degradation correspond to different pulse model parameters, respectively. The transcription rate has 6 parameters, the processing rate has 5 parameters, and the degradation rate has 4 parameters.
1 2 | estimateParams(labexon, totexon, totintr, TimeGrid, tL,
clusterNumber = NULL, loopnumber = 50, message = TRUE)
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labexon |
A matrix containing expression levels of 4su exons.For the calculation of the expression value, see |
totexon |
A matrix containing expression levels of total exons.For the calculation of the expression value, see |
totintr |
A matrix containing expression levels of total introns.For the calculation of the expression value, see |
TimeGrid |
A vector of points in time at which experimental data is collected, not allowed to be repeated |
tL |
4sU labeled time during the experiment |
clusterNumber |
Given the number of cluster cores, the default is the maximum number of available cores |
loopnumber |
The number of iterations of the gradient descent when solving the parameter. The default is 50. |
message |
Whether to print the log, the default is TRUE |
A 'pulseTDmodel' containing the expression values of the filtered genes, a list of solved parameters, and some basic parameter information
1 2 3 4 5 6 7 8 | data('rpkmSim', package='pulseTD')
rpkm_TL <- rpkmSim$labexon[1:2,]
rpkm_PT <- rpkmSim$totintr[1:2,]
rpkm_TT <- rpkmSim$totexon[1:2,]
TimeGrid <- c(0, 15, 30, 45, 60, 75, 90, 105, 120, 135, 150, 165, 180)
tL <- 10
pulseRates<- estimateParams(rpkm_TL,rpkm_TT,rpkm_PT,TimeGrid,tL,clusterNumber=1,loopnumber=10)
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